Problems with the merge-filter.sh script

[kaivalya shevade]

Hi,

I was trying to run Fit-Hi-C on a HiC dataset. To begin with I only decided to run Fit-Hi-C on chromosome 1 of the dataset. Everything seems to have run well except the merge-filter.sh script.

Here is the command I use :

bash merge-filter.sh ~/HiC/FitHiC/Chr1_THP1_min5kb_max5mb/FitHiC.spline_pass1.res5000.significances.txt.gz 5000 ~/HiC/FitHiC/Chr1_THP1_min5kb_max5mb/filtered_Chr1_THP1 0.05 ~/HiC/FitHiC/fithic/fithic/utils

The script seems to recognize all inputs but gets stuck after this dialogue 

 *** bin_size:  5000

 *** headerInp:  0

 *** connectivity_rule:  8

 *** TopPctElem:  100

 *** NeighborHoodBinThr:  10000

 *** QValCol:  7

 *** PValCol:  6

 *** SortOrder:  0

OutDir:  /home/kaivalyashevade/HiC/FitHiC/Chr1_THP1_min5kb_max5mb

temp_ChrName_File:  /home/kaivalyashevade/HiC/FitHiC/Chr1_THP1_min5kb_max5mb/filtered_Chr1_THP_chrName.bed

List of chromosomes considered:  ['chr1']

Processing the chromosome:  chr1

zcat /home/kaivalyashevade/HiC/FitHiC/Chr1_THP1_min5kb_max5mb/fithic_subset.gz | awk '{if ($1=="chr1" && $3=="chr1"){print $0}}' -  > /home/kaivalyashevade/HiC/FitHiC/Chr1_THP1_min5kb_max5mb/Temp_chr1_Dump.bed

Number of interactions for the current chromosome:  6971872

Extracted interactions for the current chromosome 

After this it neither exits nor adds anything to the output file.

Do you know what might be the error here ?

Thanks,

Kaivalya